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Yorodumi- PDB-3u8u: Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ap... -
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-Basic information
Entry | Database: PDB / ID: 3u8u | ||||||
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Title | Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form | ||||||
Components | DNA-(apurinic or apyrimidinic site) lyase | ||||||
Keywords | HYDROLASE / LYASE / Endonuclease | ||||||
Function / homology | Function and homology information Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / phosphodiesterase I activity / double-stranded DNA 3'-5' DNA exonuclease activity ...Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / phosphodiesterase I activity / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / positive regulation of gene expression via chromosomal CpG island demethylation / Displacement of DNA glycosylase by APEX1 / phosphoric diester hydrolase activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / uracil DNA N-glycosylase activity / DNA catabolic process / 3'-5'-DNA exonuclease activity / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / DNA-(apurinic or apyrimidinic site) endonuclease activity / regulation of mRNA stability / 3'-5' exonuclease activity / telomere maintenance / base-excision repair, gap-filling / cell redox homeostasis / DNA endonuclease activity / base-excision repair / chromatin DNA binding / transcription corepressor activity / RNA-DNA hybrid ribonuclease activity / regulation of apoptotic process / DNA recombination / endonuclease activity / chromosome, telomeric region / damaged DNA binding / transcription coactivator activity / oxidoreductase activity / ribosome / nuclear speck / DNA repair / centrosome / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Agarwal, R. / Naidu, M.D. | ||||||
Citation | Journal: To be Published Title: Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form Authors: Agarwal, R. / Naidu, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u8u.cif.gz | 342.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u8u.ent.gz | 276.6 KB | Display | PDB format |
PDBx/mmJSON format | 3u8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u8u_validation.pdf.gz | 474.7 KB | Display | wwPDB validaton report |
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Full document | 3u8u_full_validation.pdf.gz | 495.5 KB | Display | |
Data in XML | 3u8u_validation.xml.gz | 67.3 KB | Display | |
Data in CIF | 3u8u_validation.cif.gz | 94.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/3u8u ftp://data.pdbj.org/pub/pdb/validation_reports/u8/3u8u | HTTPS FTP |
-Related structure data
Related structure data | 1hd7S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 35606.492 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APEX1, APE, APE1, APEX, APX, HAP1, REF1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL References: UniProt: P27695, Hydrolases; Acting on ester bonds, DNA-(apurinic or apyrimidinic site) lyase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.34 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.05M MGCL2.6H2O, 0.1M HEPES PH 7.5, 30% PEG 550MME, 1 MICRO-MOLAR HYCANTHONE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 280K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2007 / Details: mirrors |
Radiation | Monochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. all: 131267 / Num. obs: 131267 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.5 / Num. unique all: 12822 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HD7 Resolution: 2.15→40.71 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.577 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.823 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→40.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.149→2.205 Å / Total num. of bins used: 20
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